Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist. Command: run_dada_paired.R /tmp/tmpit99unn6/forward /tmp/tmpit99unn6/reverse /tmp/tmpit99unn6/output.tsv.biom /tmp/tmpit99unn6/track.tsv /tmp/tmpit99unn6/filt_f /tmp/tmpit99unn6/filt_r 296 286 0 0 2.0 2.0 2 consensus 1.0 1 1000000 R version 3.5.1 (2018-07-02) Loading required package: Rcpp DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3 1) Filtering ........................ 2) Learning Error Rates 257932032 total bases in 871392 reads from 24 samples will be used for learning the error rates. Traceback (most recent call last): File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 234, in denoise_paired run_commands([cmd]) File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands subprocess.run(cmd, check=True) File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpit99unn6/forward', '/tmp/tmpit99unn6/reverse', '/tmp/tmpit99unn6/output.tsv.biom', '/tmp/tmpit99unn6/track.tsv', '/tmp/tmpit99unn6/filt_f', '/tmp/tmpit99unn6/filt_r', '296', '286', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' died with . During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__ results = action(**arguments) File "", line 2, in denoise_paired File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable output_types, provenance) File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_ output_views = self._callable(**view_args) File "/home/yudahai/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 249, in denoise_paired " and stderr to learn more." % e.returncode) Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.